We present contrast enhancement for the autofluorescing coenzymes flavin adenine dinucleotide (FAD) and nicotinamide adenine dinucleotide (NADH) in glycerol using phase and polarization shaped laser pulses after the transmission through a kagome fiber. Thereto, we report a way to calculate the optimal light modulator incident polarization angle, which in general differs from the horizontal. Combining phase and polarization shaping, we can selectively excite FAD in one polarization and simultaneously NADH in the other polarization direction by third order phase functions. Due to high anisotropy, the contrast of the fluorescence depends on the polarization direction. The effect of the fiber on the phase is precompensated in order to obtain the desired phase function after the fiber. Since the relative amounts of NADH and FAD give information about cellular metabolic activity which in turn helps understand disease processes, the method promises high biophotonic potential
